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Since my original post I have found another source where this technique is not required, i.e. no header to worry about.
But if anyone else has a suggestion, I'd be glad to hear it as I'm sure I could find uses for it in the future.
//put your scrolling code here targetting the 'popup' window.
//Use the scrolling methods tedster mentioned.
popup = window.open("www.yoururl.com/page.htm","popup")
//you'll need to browser sniff here:
window.top.popup.attachEvent('onload',goScroll) //this one for IE
window.top.popup.onLoad = goScroll() //this one for netscape nav
This *should* work and should avoid any parsing.